JAL-1270 test suits import order refactor

[jalview.git] / test / jalview / datamodel / AlignmentAnnotationTests.java

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index f23b3d2..4c9eabe 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,10 +1,12 @@
 package jalview.datamodel;
 
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
 import jalview.analysis.AlignSeq;
 import jalview.io.AppletFormatAdapter;
 
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class AlignmentAnnotationTests
 {
@@ -153,7 +155,48 @@ public class AlignmentAnnotationTests
                       : "Out of range");
       assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
     }
-    // new jalview.io.FormatAdapter().formatSequences("STOCKHOLM", n)
   }
 
+  @Test
+  public void testAdjustForAlignment()
+  {
+    SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
+    seq.createDatasetSequence();
+
+    /*
+     * Annotate positions 3/4/5 (CDE) with values 1/2/3
+     */
+    Annotation[] anns = new Annotation[]
+    { null, null, new Annotation(1), new Annotation(2), new Annotation(3) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", anns);
+    seq.addAlignmentAnnotation(ann);
+
+    /*
+     * Check annotation map before modifying aligned sequence
+     */
+    assertNull(ann.getAnnotationForPosition(1));
+    assertNull(ann.getAnnotationForPosition(2));
+    assertNull(ann.getAnnotationForPosition(6));
+    assertNull(ann.getAnnotationForPosition(7));
+    assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
+    assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
+    assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
+
+    /*
+     * Trim the displayed sequence to BCD and adjust annotations
+     */
+    seq.setSequence("BCD");
+    seq.setStart(2);
+    seq.setEnd(4);
+    ann.adjustForAlignment();
+
+    /*
+     * Should now have annotations for aligned positions 2, 3Q (CD) only
+     */
+    assertEquals(3, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertEquals(1, ann.annotations[1].value, 0.001);
+    assertEquals(2, ann.annotations[2].value, 0.001);
+  }
 }